User: martin.busch

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Posts by martin.busch

<prev • 8 results • page 1 of 1 • next >
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Comment: C: ReactomePA / Reactome: GSEA error message
... Thank you so much for your comment - in fact I was pretty suprised to see that the result was true - something that should not have happened. There was some mapping involved and it seems that multiple ensembl IDs can be mapped to one entrez ID. I thought that I had this sorted out. Anyways, not it w ...
written 1 day ago by martin.busch0
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ReactomePA / Reactome: GSEA error message
... Hi everyone, I am sorry to ask another question, however, there is an error message that keeps me puzzled. When passing over a list of human entrez IDs to reactomePA for GSEA using result <- gsePathway(anaData, nPerm=10000, pvalueCutoff=0.2, pAdjustMethod="BH", verbose=FALSE) Rstudio becomes ...
reactome gsea reactomepa fgsea written 1 day ago by martin.busch0
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Comment: C: ReactomePA / Reactome: Crash when plotting
... Thanks for your help, I will try to implement your script.   Best, Martin ...
written 6 days ago by martin.busch0
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Comment: C: ReactomePA / Reactome: Crash when plotting
... Thank your for getting in touch. The version I am using is 1.24.0. An example would be the following: rm(list=ls()) library(ReactomePA) dataSets <- c("http://martin-busch.com/work/set1.csv", "http://martin-busch.com/work/set2.csv", "http://martin-busch.com/work/set3 ...
written 6 days ago by martin.busch0
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ReactomePA / Reactome: Crash when plotting
... Hi everybody, ReactomePA used to work fine in my handy, however, when trying to plot results it recently started to crash Rstudio completely. I cannot see an appearent reason, e.g. I can dotplot a result, but using emapplot of the same result one line of code later it completely crashes. Ocassional ...
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Comment: C: ReactomePA / Reactome: Extraction of genes within a term
... Thanks a lot for your help! ...
written 27 days ago by martin.busch0
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Comment: C: ReactomePA / Reactome: Extraction of genes within a term
... Thank you for your swift reply, that works perfectly fine. Since I am quite new to R, I am a bit confused with the data format of x Using geneInCategory(x)[] I can extract all categories, but is it somehow possible to extract only a subset, e.g. those with p< 0.05 ? Thanks for your help! ...
written 27 days ago by martin.busch0
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ReactomePA / Reactome: Extraction of genes within a term
... Hi all, Currently I use the ReactomePA package for functional/athway analysis and I get a couple of significantly enriched terms in my data. However, I am wondering which particular genes from my data are represented in these terms - is there an elegant way to extract the gene ids/names of all gene ...
pathways reactomepa functional annotation written 27 days ago by martin.busch0 • updated 27 days ago by Guangchuang Yu990

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